Course book: Chapter 4 "The structure of DNA" Flashcards
According to convention, do you write a DNA sequence 5’ –> 3’ or the other way around?
5’ –> 3’, which is also the direction of growth of oligonucleotides.
Which bases are purines?
Adenine, guanine
Which bases are pyrimidines?
Thymine, Cytosine
What’s tautomerization? How is it relevant for nucleotides?
Tautomerization is when a proton is moved from one site to another in a molecule. A molecule can have several tautomeric forms. Each nucleotide has a tautomeric form.
For purines (AG), the nitrogen which is incorporated in their ring structure can be protonized.
For pyrimidines (TC), the oxygen can be protonized.
What’s the driving force of base stacking?
Base stacking is powered by hydrophobic interactions.
Why is the distance between the bases so important for hydrogen bonding in vivo?
If the distance is too far, water molecule(s) will be able to fit in between them, acting as a H-donor and/or H-acceptor.
Is the following statement true?
DNA is usually a right handed molecule.
Yes. The strands follow your fingers when holding it with the thumb pointing upwards.
Why is the major groove more information dense than the minor groove?
The major groove is wider and deeper, allowing amino acids to probe it more efficiently. It allows enzymes to decipher exactly what base pairs are present by finding the factors which are listed below. They can even distinguish between AT / TA and GC / CG.
There are four characteristics that can be seen in the major groove:
- Hydrogen bond acceptor
- Hydrogen bond donor
- Methyl group
- Non-polar hydrogen group
What 3 kinds of DNA helices are there?
A, B, Z
Most dense (11bp/turn) –> less dense (10bp/turn) –> least dense
The number of nucleotides per turn is physiologically ~10.5. The difference between the practical and theoretical value is thought to be due to local irregularities, where propeller twists can occur. These propeller twists occur if two complementary bases arent properly aligned with each other (this changes the characteristics of the major- and minor groove).
How can DNA form a left-handed helix?
The glycosidic bond between the 2’deoxyribose and the nitrogen base can occur in two conformations, “anti” and “syn”. If the DNA sequence contain bases cycling from “syn” to “anti”, the Z-form DNA will take place.
The utility of Z-DNA is unknown.
